I got the file and I put it in SR4 directory (Saints Row 4\sr3DEF_PROFILE) but it's still not saving the Options. Do I need to put it in a subfolder?

No, it is supposed to be in the same directory as the executable. That behaviour is very strange since the game obviously does refuse to even edit the file to save the options. Could you post a screenshot of the game directory showing the file size as well? I could compare if you really are using the correct version with this.

Edit: there is an even easier way to find out. Look into the registry and see if you can find the key

HKEY_LOCAL_MACHINE/SOFTWARE/GOG.com/Games/2037689757
or
HKEY_LOCAL_MACHINE/SOFTWARE/Wow6432Node/GOG.com/Games/2037689757

Open it and look at the version number shown under "ver". It should show 20170523

Thanks for looking into this!

I checked in the Registry and verified the game is version 20170523. The sr3DEF_PROFILE file is about 17 KB. The whole SR4 folder is about 9.9 GB.

I'm not sure why the Options still aren't working properly. Maybe it doesn't like the older save file I'm using. But I'm about halfway through the game and I'd rather not have to start over again.

It's hard to imagine that your old save file is the reason for your problem but there is a possibility to test this without deleting the saves - so you can be sure if this is the problem or not. Simply rename the folder containing your save files and start the game. If options are then saved correctly you can be sure that the saves are the problem so no need to try to fix this issue in another way.

Well there still is one possibility: the options are saved in the file I posted (that is for sure) so you could just PM me some screenshots of your desired settings (only those who are not saved yet of course). I could then mirror those settings with my game and upload you the required config file. It's nothing more than a workaround but it might prevent you from having to change them every time you start a game.

I sent you a message with the Option information. I hope that helps!

Also make sure you've opened a support ticket with GOG regarding this.

Also I'm really curious as to what could be causing this issue.

Can I ask you to post some info regarding your system and SR4 installation?

Basically the OS you're running (i.e. Win7 Home Premium 64-bits) and the full path to where the game is installed (C:\Whatever\Saints Row 4\) would be a good starting point.

Yes, seeing that this has been fixed for pretty everyone does really make one curios doesn't it? At least fo me such things do feel like a challenge (as well as an opportunity to help of course). So far I have hit a brick wall and I am really excited to see if you will find out more.

Well this issue is still persistent on my machine, any ideas on how to find out what the issue is?

Does it require a clean install?

Did you use Galaxy or the offline installer?

Galaxy should get the whole patching process sorted out, but with offline installers it might be worth it to make sure you've downloaded the latest version of the installer and do a clean install.

Additionally, the file containing user-selected options is written to the game's installation directory, so if you installed it somewhere where admin rights are needed to to modify files and the game isn't running with admin rights, that could also be the cause of the problem. (and in that case it would affect savegames as well)

My saves are still fine, a clean install = deleting it entirely or just overwriting it?

Run the install as admin?

Don't worry. If you uninstall the game you won't delete your savegames if you answer the question about them asked during uninstall correctly ("do you want to keep savegames?" or so). The savegames are not stored in the game folder itself. Also no need to run the installation as admin you (maybe) just need to launch the game as admin. The game is trying to write the file in which the option setting is saved the moment it is started.

The savegames are stored in a sub-directory of the game's installation folders however (at least for me they are), so don't actually delete the whole directory after you uninstall the game. Or at least make a backup of the sub-directory named "_saves".

I'll never understand games that keep saves, config files, etc. in the installation folder. Makes it a huge pain to back up manually and increases the risk of stuff getting deleted by accident.